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Top Forums UNIX for Beginners Questions & Answers Read line and save fields as variables Post 302979027 by Splinter479 on Monday 8th of August 2016 05:36:17 AM
Old 08-08-2016
thanks so far for your replies. I kind of have the feeling too that it is somehow related to the calls.txt
I thought the minimal example would do the job, but let's give you a more real copy of what I have done:

my.sh :
Code:
#!/bin/bash
echo " I AM OUTSIDE THE LOOP"

infile="calls.txt"

while IFS=',' read -r f1 f2 f3 f4 f5 f6 f7 f8 f9 f10 f11 f12 f13 f14 f15 f16 f17 f18 f19
do
        echo " I AM INSIDE THE LOOP"

        my_file1=$f1
        species1=$f2
        chrom1=$f3
        my_file2=$f4
        species2=$f5
        chrom2=$f6
        binSize=$f7
        foo1=$f8
        foo2=$f9
        foo3=$f10
        foo4=$f11
        variance=$f12
        bar1=$f13
        bar2=$f14
        java_jar=$f15
        bar3=$f16
        bar4=$f17
        unit=$f18
        bar5=$f19

        # program calls here

done < "$infile"

my calls.txt is just a one liner right now, but later many lines according to the same format shall follow:
Code:
/path/to/my/file.txt,string1,string2,/path/to/my/other/file.txt,string3,string4,int1,string5,string6,int2,int3,int4,/path/to/a/third/file.txt,path/to/a/fourth/file.txt,/path/to/a/java.jar,anotherString,anotherString,anotherString,aFloatNumber

so this is exactly a renamed representation of the calls.txt. Sorry for the censorship, but in fact I am currently developing a software tool I am ofc not allowed to share everything in detail :/

I came up with the thoughts of maybe the paths messing it up? I 'll retry with quoting the paths. Other ideas?

EDIT: quoting didn't help :/
 

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smccompile(1M)						  System Administration Commands					    smccompile(1M)

NAME
smccompile - build class list and compile Solaris Management Console service beans for remote use SYNOPSIS
/usr/sadm/bin/smccompile -c beanname /usr/sadm/bin/smccompile -j tool | service [-n altjarname] jarfile /usr/sadm/bin/smccompile -j library [-n altjarname] ALLTOOL | ALLSERVICE | ALL | attachedBeanname jarfile DESCRIPTION
The smccompile command is used by developers of tools, services, and libraries for the Solaris Management Console. For information regard- ing the Solaris Management Console, see smc(1M). smccompile compiles service class files given by the bean name for use with the Solaris Management Console. This step builds the extra proxy and stub classes for services to be used with Solaris Management Console tools. Solaris Management Console requires running smccom- pile -c before creating service jar files, and smccompile -j after creating tool, service, and library jars. smccompile, in conjunction with smcregister(1M), is intended to replace the smcconf command as the preferred interface for managing the Solaris Management Console repository as well as toolboxes from within scripts, due to significant performance enhancements over smcconf. OPTIONS
The following options are supported: ALL Specify that the library being registered to or unregistered from the repository is for use by all tools and services. ALLSERVICE Specify that the library being registered to or unregistered from the repository is for use by all services. ALLTOOL Specify that the library being registered to or unregistered from the repository is for use by all tools. attachedBeaname Specify the name of a registered jar to which the library jarfile should be attached to (or detached from). This is typi- cally the same as altjarname (if provided) or jarfile used to register the jar to which this library is being attached or detached. An attached library means the library is only available for use by the tool or service to which it is being attached. beanname The full package path of the bean name to be compiled. An example bean name is: com.mycompany.myproduct.MyService. -c Compile and build service class files for the specified bean name. This step builds the extra proxy and stub classes for services to be used with Solaris Management Console tools. You must run smccompile with this option before creating service type jar files. -j Build a list of classes in text format, suitable as input to smcregister for registration with the Solaris Management Con- sole repository. The output is written to standard out and should be redirected to a file. You must run smccompile with this option after creating any tool, service, or library jar. jarfile Specify the full path to the jar file to be registered. The name must be in the form beanname.jar, where beanname is the package path to the bean. If it is not, an alternate name must be given in that form using the -n option. -n altjarname Rename the jarfile in the repository to altjarname. Typically. this is the full bean name. For example, if the jarfile was MyTool.jar, then altjarname might be com.mycompany.myproduct.MyTool.jar. It is recommended that an altjarname containing the full package path be used. You must use this same name when registering the jar with smcregister. EXAMPLES
Example 1: Compiling a Service The following command takes a Solaris Management Console service and builds its proxy and stub classes to make the service usable by Solaris Management Console tools: /usr/sadm/bin/smccompile -c com.mycompany.myproject.MyServiceImpl Example 2: Building a Class List for a Service The following command builds the class list file (classlist.txt) for a service suitable for use with the smcregister(1M) command: /usr/sadm/bin/smccompile -j service -n com.mycompany.myproject.MyServiceImpl.jar ${HOME}/workarea/MyServiceImpl.jar > classlist.txt The following command does the same thing without specifying an alternate name: /usr/sadm/bin/smccompile -j service ${HOME}/workarea/com.mycompany.myproject.MyServiceImpl.jar > classlist.txt Example 3: Building a Class List for a Tool The following command builds the class list file (classlist.txt) for a tool suitable for use with the smcregister(1M) command: /usr/sadm/bin/smccompile -j tool -n com.mycompany.myproject.MyTool.jar ${HOME}/workarea/MyTool.jar > classlist.txt The following command does the same thing without specifying an alternate name: /usr/sadm/bin/smccompile -j tool ${HOME}/workarea/com.mycompany.myproject.MyTool.jar > classlist.txt Example 4: Building a Class List for a Library Attached to All Tools The following command builds the class list file (classlist.txt) for a library suitable for use with the smcregister(1M) command, and is attached to all tools: /usr/sadm/bin/smccompile -j library -n com.mycompany.myproject.MyLibrary.jar ALLTOOL ${HOME}/workarea/MyLibrary.jar > classlist.txt The following command does the same thing without specifying an alternate name: /usr/sadm/bin/smccompile -j library ALLTOOL ${HOME}/workarea/com.mycompany.myproject.MyLibrary.jar > classlist.txt Example 5: Building a Class List for a Library Attached to a Specific Tool The following command builds the class list file (classlist.txt) for a library suitable for use with the smcregister(1M) command, and is attached to a specific tool: /usr/sadm/bin/smccompile -j library -n com.mycompany.myproject.MyLibrary.jar com.mycompany.myproject.MyTool.jar ${HOME}/workarea/MyLibrary.jar > classlist.txt The following command does the same thing without specifying an alternate name: /usr/sadm/bin/smccompile -j library com.mycompany.myproject.MyTool.jar ${HOME}/workarea/com.mycompany.myproject.MyLibrary.jar > classlist.txt ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of smccompile: JAVA_HOME If you do not specify this environment variable, your PATH is searched for a suitable java. Otherwise, the /usr/j2se location is used. EXIT STATUS
The following exit values are returned: 0 Successful completion. 1 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWMc | +-----------------------------+-----------------------------+ SEE ALSO
smc(1M), smcconf(1M), smcregister(1M), attributes(5), environ(5) NOTES
All standard shell quoting rules apply. SunOS 5.10 17 Jul 2001 smccompile(1M)
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